587 skills found ¡ Page 16 of 20
jaechang-hits / ddinter-databaseQuery DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for severity (major/moderate/minor), mechanisms, and clinical recommendations. No auth. For FDA labeling use dailymed-database; for pharmacogenomics use clinpgx-database.
jaechang-hits / drugbank-database-accessParse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with severity, map targets/enzymes/transporters, compute SMILES similarity. Primary via local XML; REST API rate-limited (3k/month dev).
jaechang-hits / emdb-databaseLook up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth.
jaechang-hits / fda-databaseQuery openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key.
jaechang-hits / gtopdb-databaseQuery IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth.
jaechang-hits / opentargets-databaseQuery Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
jaechang-hits / pdb-databaseQuery RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org.
jaechang-hits / pytdc-therapeutics-data-commonsTherapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET benchmarks for therapeutic ML and property prediction.
jaechang-hits / unichem-databaseCross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity.
jaechang-hits / zinc-databaseQuery the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking.
jaechang-hits / brenda-databaseBRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data. 80K+ enzymes, 7M+ values. Free academic registration. For metabolic modeling use cobrapy-metabolic-modeling; metabolites use hmdb-database.
jaechang-hits / reactome-databaseQuery Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
jaechang-hits / string-database-ppiQuery STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.
jaechang-hits / archs4-databaseQuery ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices.
jaechang-hits / cbioportal-databaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis.
jaechang-hits / clinpgx-databaseQuery the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways.
jaechang-hits / clinvar-databaseQuery NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.
jaechang-hits / cosmic-databaseQuery COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
jaechang-hits / dbsnp-databaseQuery NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key).
jaechang-hits / ena-databaseENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
jaechang-hits / encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene.
jaechang-hits / ensembl-databaseEnsembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
jaechang-hits / gene-databaseNCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.
jaechang-hits / geo-databaseNCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
jaechang-hits / gget-genomic-databasesUnified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease.
jaechang-hits / gnomad-databasegnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants.
jaechang-hits / gwas-databaseNHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.
jaechang-hits / jaspar-databaseJASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis.
jaechang-hits / kegg-databaseKEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
jaechang-hits / monarch-databaseMonarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking.
